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<title>Per Sequence Quality Scores</title>
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<h1>Per Sequence Quality Scores</h1>
<h2>Summary</h2>
<p>
The per sequence quality score report allows you to see if a subset
of your sequences have universally low quality values.  It is often
the case that a subset of sequences will have universally poor quality,
often because they are poorly imaged (on the edge of the field of view
etc), however these should represent only a small percentage of the total
sequences.
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<p><img src="per_sequence_quality.png"></p>
<p>
If a significant proportion of the sequences in a run have overall low
quality then this could indicate some kind of systematic problem - possibly
with just part of the run (for example one end of a flowcell).
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<h2>Warning</h2>
<p>
A warning is raised if the most frequently observed mean quality is below 27 -
this equates to a 0.2% error rate.
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<h2>Failure</h2>
<p>
An error is raised if the most frequently observed mean quality is below 20 -
this equates to a 1% error rate.
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